Add 85 automated E. coli SDRF annotations (batch 1)

[ypriverol]

E. coli SDRF annotations — automated batch 1 (85 datasets)

SDRF-Proteomics annotations for 85 Escherichia coli ProteomeXchange datasets
that were not previously annotated in this repository or quantms-datasets.

How they were produced

• Sample/technical metadata drafted from each project's PRIDE metadata and
  submitter sample/data-processing protocols.
• characteristics[organism] grounded to the organism PRIDE declares for the
  project (single-organism datasets only in this batch).
• Controlled-vocabulary values (instrument, label, cleavage agent, dissociation,
  acquisition method) resolved to PSI-MS accessions against the OLS ontology
  cache; any accession that failed verification was reduced to NT= only.
• All files pass parse_sdrf validate-sdrf -t ms-proteomics (warnings only, no
  errors).

Scope / review notes

• First-pass automated annotations — review welcome. Known residuals: a few
  characteristics[organism part] terms and instrument name casing may warrant
  refinement.
• Empirical verification of instrument / mass tolerances / dissociation from the
  raw spectra is a planned follow-up pass.
• Multi-organism E. coli datasets are intentionally deferred to a later batch.

Summary by CodeRabbit

• Documentation
  • Added status notes for multiple sandboxed datasets.
  • Documented blockers, including unresolved chemistry annotations and missing channel-to-sample mapping evidence.
  • Recorded criteria for validation, evidence recovery, and returning datasets to the main dataset area.

[coderabbitai]

Important

Review skipped

Review was skipped due to path filters

⛔ Files ignored due to path filters (8)

• datasets/PXD006474/PXD006474.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD007207/PXD007207.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD009595/PXD009595.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD009773/PXD009773.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD010014/PXD010014.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD010988/PXD010988.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD012553/PXD012553.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD014359/PXD014359.sdrf.tsv is excluded by !**/*.tsv

CodeRabbit blocks several paths by default. You can override this behavior by explicitly including those paths in the path filters. For example, including **/dist/** will override the default block on the dist directory, by removing the pattern from both the lists.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 0b7351a2-4034-434e-acfc-d2ce66e49b1c

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

📝 Walkthrough

Walkthrough

Adds sandbox status notes for ten datasets, documenting unresolved chemistry normalization or TMT channel-mapping evidence issues and specifying SDRF validation and dataset move-back criteria.

Changes

Sandbox status documentation

Layer / File(s)	Summary
Parked dataset status and return criteria sandbox/PXD002409/notes.md, sandbox/PXD002705/notes.md, sandbox/PXD010402/notes.md, sandbox/PXD014039/notes.md, sandbox/PXD016403/notes.md, sandbox/PXD029140/notes.md, sandbox/PXD035326/notes.md, sandbox/PXD040618/notes.md, sandbox/PXD045656/notes.md, sandbox/PXD053317/notes.md	Adds notes describing each dataset’s parked status, unresolved evidence or normalization issue, required SDRF validation command, and conditional relocation back to datasets/.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Suggested reviewers: timosachsenberg

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly matches the main change: adding 85 automated E. coli SDRF annotations for batch 1.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch annotate/ecoli-batch-1

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